applications/nanoparticleBuilder/nanoparticleBuilder.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */

#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <cmath>
#include <iostream>
#include <string>
#include <map>
#include <fstream>
#include <algorithm>

#include "config.h"
#include "shapedLatticeSpherical.hpp"
#include "nanoparticleBuilderCmd.h"
#include "lattice/LatticeFactory.hpp"
#include "utils/MoLocator.hpp"
#include "lattice/Lattice.hpp"
#include "brains/Register.hpp"
#include "brains/SimInfo.hpp"
#include "brains/SimCreator.hpp"
#include "io/DumpWriter.hpp"
#include "math/Vector3.hpp"
#include "math/SquareMatrix3.hpp"
#include "utils/StringUtils.hpp"

using namespace std;
using namespace oopse;
void createMdFile(const std::string&oldMdFileName, 
                  const std::string&newMdFileName,
                  int components,int* numMol);

int main(int argc, char *argv []) {
  
  //register force fields
  registerForceFields();
  registerLattice();
  
  gengetopt_args_info args_info;
  std::string latticeType;
  std::string inputFileName;
  std::string outPrefix;
  std::string outMdFileName;
  std::string outInitFileName;

  
  Lattice *simpleLat;
  MoLocator* locator;
  int* numMol;
  int nComponents;
  double latticeConstant;
  std::vector<double> lc;
  double mass;
  const double rhoConvertConst = 1.661;
  double density;
  double particleRadius;
  
  
  Mat3x3d hmat;
  std::vector<Vector3d> latticePos;
  std::vector<Vector3d> latticeOrt;
  int numMolPerCell;
  int nShells; /* Number of shells in nanoparticle*/
  int numSites;
  
  DumpWriter *writer;
  
  // Parse Command Line Arguments
  if (cmdline_parser(argc, argv, &args_info) != 0)
    exit(1);
  
        
  /* get lattice type */
  latticeType = UpperCase(args_info.latticetype_arg);
    
  /* get input file name */
  if (args_info.inputs_num)
    inputFileName = args_info.inputs[0];
  else {
    std::cerr << "You must specify a input file name.\n" << std::endl;
    cmdline_parser_print_help();
    exit(1);
  }
  
  /* parse md file and set up the system */
  SimCreator oldCreator;
  SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
  
  
  /*calculate lattice constant (in Angstrom)
  latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
                        1.0 / 3.0);*/
  
  latticeConstant = args_info.latticeCnst_arg;
  particleRadius = args_info.radius_arg;
  Globals* simParams = oldInfo->getSimParams();
  
  /* Find out how many different components in this simualtion */
  nComponents =simParams->getNComponents();
  
  /*determine the output file names*/
  if (args_info.output_given){
    outInitFileName = args_info.output_arg;
  }else{
    outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
  }
   
  
  /* create Molocators */
  locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
  
  /* Create nanoparticle */
  shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius);
  /* Build a lattice and get lattice points for this lattice constant */
  vector<Vector3d> nanoParticleSites = nanoParticle.getPoints();
  /* Get number of lattice sites */
  numSites = nanoParticleSites.size();
 
  numMol = new int[nComponents];
 
  
  /* Random particle is the default case*/
  if (!args_info.ShellRadius_given){
    std::cout << "Creating a random nanoparticle" << std::endl;
    /* Check to see if we have enough components */
    if (nComponents != args_info.molFraction_given + 1){
      std::cerr << "Number of components does not equal molFraction occurances." << std::endl;
      exit(1);
    }
    /* Build the mole fractions and number of molecules of each type */   
    int totComponents = 0;
    for (int i = 0;i<nComponents-2;i++){ /* Figure out Percent for each component */
      numMol[i] = int((double)numSites * args_info.molFraction_arg[i]);
      totComponents += numMol[i];
    }
    numMol[nComponents-1] = numSites - totComponents;
        /* do the iPod thing, Shuffle da vector */
        std::random_shuffle(nanoParticleSites.begin(), nanoParticleSites.end());
  } else{ /*Handle core-shell with multiple components.*/
    std::cout << "Creating a core-shell nanoparticle." << std::endl;
    if (nComponents != args_info.ShellRadius_given + 1){
      std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl;
      exit(1);
    }   
    
  }


   //get the orientation of the cell sites
  //for the same type of molecule in same lattice, it will not change
   latticeOrt = nanoParticle.getPointsOrt();
  
  
  // needed for writing out new md file.
  
    outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
    outMdFileName = outPrefix + ".md";
  
    //creat new .md file on fly which corrects the number of molecule     
    createMdFile(inputFileName, outMdFileName, nComponents,numMol);
  
  if (oldInfo != NULL)
    delete oldInfo;
  
  
  // We need to read in new siminfo object.     
  //parse md file and set up the system
  //SimCreator NewCreator;
  
  SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
  
  
  // Place molecules
  Molecule* mol;
  SimInfo::MoleculeIterator mi;
  mol = NewInfo->beginMolecule(mi);
 int l = 0;
 for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) {
        locator->placeMol(latticePos[l], latticeOrt[l], mol);
        l++;
  }


  //fill Hmat
  hmat(0, 0)=  latticeConstant;
  hmat(0, 1) = 0.0;
  hmat(0, 2) = 0.0;
  
  hmat(1, 0) = 0.0;
  hmat(1, 1) =  latticeConstant;
  hmat(1, 2) = 0.0;
  
  hmat(2, 0) = 0.0;
  hmat(2, 1) = 0.0;
  hmat(2, 2) =  latticeConstant;
  
  //set Hmat
  NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
  
  
  //create dumpwriter and write out the coordinates
  NewInfo->setFinalConfigFileName(outInitFileName);
  writer = new DumpWriter(NewInfo);
  
  if (writer == NULL) {
    std::cerr << "error in creating DumpWriter" << std::endl;
    exit(1);
  }
  
  writer->writeDump();
  std::cout << "new initial configuration file: " << outInitFileName
            << " is generated." << std::endl;
  
  //delete objects
  
  //delete oldInfo and oldSimSetup
  
  if (NewInfo != NULL)
    delete NewInfo;
  
  if (writer != NULL)
    delete writer;      
  cmdline_parser_free(&args_info);
  return 0;
}

void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
                  int components,int* numMol) {
  ifstream oldMdFile;
  ofstream newMdFile;
  const int MAXLEN = 65535;
  char buffer[MAXLEN];
  
  //create new .md file based on old .md file
  oldMdFile.open(oldMdFileName.c_str());
  newMdFile.open(newMdFileName.c_str());
  
  oldMdFile.getline(buffer, MAXLEN);
 
  int i = 0;
  while (!oldMdFile.eof()) {
    
    //correct molecule number
    if (strstr(buffer, "nMol") != NULL) {
        if(i<components){
      sprintf(buffer, "\tnMol = %i;", numMol[i]);                               
      newMdFile << buffer << std::endl;
      i++;
        }
    } else
      newMdFile << buffer << std::endl;
    
    oldMdFile.getline(buffer, MAXLEN);
  }
  
  oldMdFile.close();
  newMdFile.close();
}

Revision:	2657
Committed:	Wed Mar 22 20:57:09 2006 UTC (18 years, 5 months ago) by chuckv
File size:	9093 byte(s)
Log Message:	Added shaped lattice.
#	User	Rev	Content
1	chuckv	2352	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include <cstdlib>
43			#include <cstdio>
44			#include <cstring>
45			#include <cmath>
46			#include <iostream>
47			#include <string>
48			#include <map>
49			#include <fstream>
50	chuckv	2657	#include <algorithm>
51	chuckv	2352
52			#include "config.h"
53	chuckv	2657	#include "shapedLatticeSpherical.hpp"
54	chuckv	2352	#include "nanoparticleBuilderCmd.h"
55			#include "lattice/LatticeFactory.hpp"
56			#include "utils/MoLocator.hpp"
57			#include "lattice/Lattice.hpp"
58			#include "brains/Register.hpp"
59			#include "brains/SimInfo.hpp"
60			#include "brains/SimCreator.hpp"
61			#include "io/DumpWriter.hpp"
62			#include "math/Vector3.hpp"
63			#include "math/SquareMatrix3.hpp"
64			#include "utils/StringUtils.hpp"
65
66			using namespace std;
67			using namespace oopse;
68			void createMdFile(const std::string&oldMdFileName,
69			const std::string&newMdFileName,
70	chuckv	2657	int components,int* numMol);
71	chuckv	2352
72			int main(int argc, char *argv []) {
73
74			//register force fields
75			registerForceFields();
76			registerLattice();
77
78			gengetopt_args_info args_info;
79			std::string latticeType;
80			std::string inputFileName;
81			std::string outPrefix;
82			std::string outMdFileName;
83			std::string outInitFileName;
84
85
86
87			Lattice *simpleLat;
88	chuckv	2657	MoLocator* locator;
89			int* numMol;
90			int nComponents;
91	chuckv	2352	double latticeConstant;
92			std::vector<double> lc;
93			double mass;
94			const double rhoConvertConst = 1.661;
95			double density;
96	chuckv	2657	double particleRadius;
97	chuckv	2352
98
99
100			Mat3x3d hmat;
101			std::vector<Vector3d> latticePos;
102			std::vector<Vector3d> latticeOrt;
103			int numMolPerCell;
104			int nShells; /* Number of shells in nanoparticle*/
105			int numSites;
106
107			DumpWriter *writer;
108
109	chuckv	2574	// Parse Command Line Arguments
110	chuckv	2352	if (cmdline_parser(argc, argv, &args_info) != 0)
111			exit(1);
112
113
114
115			/* get lattice type */
116			latticeType = UpperCase(args_info.latticetype_arg);
117
118			/* get input file name */
119			if (args_info.inputs_num)
120			inputFileName = args_info.inputs[0];
121			else {
122			std::cerr << "You must specify a input file name.\n" << std::endl;
123			cmdline_parser_print_help();
124			exit(1);
125			}
126
127			/* parse md file and set up the system */
128			SimCreator oldCreator;
129			SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
130
131
132			/*calculate lattice constant (in Angstrom)
133			latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density,
134			1.0 / 3.0);*/
135
136			latticeConstant = args_info.latticeCnst_arg;
137			particleRadius = args_info.radius_arg;
138	chuckv	2657	Globals* simParams = oldInfo->getSimParams();
139	chuckv	2352
140	chuckv	2657	/* Find out how many different components in this simualtion */
141			nComponents =simParams->getNComponents();
142	chuckv	2352
143			/determine the output file names/
144	chuckv	2574	if (args_info.output_given){
145	chuckv	2352	outInitFileName = args_info.output_arg;
146	chuckv	2574	}else{
147	chuckv	2352	outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
148	chuckv	2574	}
149	chuckv	2657
150	chuckv	2352
151
152			/* create Molocators */
153			locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
154
155	chuckv	2657	/* Create nanoparticle */
156			shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius);
157			/* Build a lattice and get lattice points for this lattice constant */
158			vector<Vector3d> nanoParticleSites = nanoParticle.getPoints();
159			/* Get number of lattice sites */
160			numSites = nanoParticleSites.size();
161
162			numMol = new int[nComponents];
163
164	chuckv	2352
165			/* Random particle is the default case*/
166			if (!args_info.ShellRadius_given){
167			std::cout << "Creating a random nanoparticle" << std::endl;
168			/* Check to see if we have enough components */
169			if (nComponents != args_info.molFraction_given + 1){
170			std::cerr << "Number of components does not equal molFraction occurances." << std::endl;
171	chuckv	2657	exit(1);
172	chuckv	2352	}
173	chuckv	2657	/* Build the mole fractions and number of molecules of each type */
174	chuckv	2352	int totComponents = 0;
175			for (int i = 0;i<nComponents-2;i++){ /* Figure out Percent for each component */
176			numMol[i] = int((double)numSites * args_info.molFraction_arg[i]);
177			totComponents += numMol[i];
178			}
179			numMol[nComponents-1] = numSites - totComponents;
180	chuckv	2657	/* do the iPod thing, Shuffle da vector */
181			std::random_shuffle(nanoParticleSites.begin(), nanoParticleSites.end());
182	chuckv	2352	} else{ /Handle core-shell with multiple components./
183			std::cout << "Creating a core-shell nanoparticle." << std::endl;
184			if (nComponents != args_info.ShellRadius_given + 1){
185			std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl;
186	chuckv	2657	exit(1);
187			}
188	chuckv	2352
189			}
190
191	chuckv	2657
192	chuckv	2352	//get the orientation of the cell sites
193			//for the same type of molecule in same lattice, it will not change
194	chuckv	2657	latticeOrt = nanoParticle.getPointsOrt();
195	chuckv	2352
196
197
198			// needed for writing out new md file.
199
200			outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
201			outMdFileName = outPrefix + ".md";
202
203			//creat new .md file on fly which corrects the number of molecule
204	chuckv	2657	createMdFile(inputFileName, outMdFileName, nComponents,numMol);
205	chuckv	2352
206			if (oldInfo != NULL)
207			delete oldInfo;
208
209
210			// We need to read in new siminfo object.
211			//parse md file and set up the system
212			//SimCreator NewCreator;
213
214			SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
215
216
217	chuckv	2657	// Place molecules
218	chuckv	2352	Molecule* mol;
219			SimInfo::MoleculeIterator mi;
220			mol = NewInfo->beginMolecule(mi);
221	chuckv	2657	int l = 0;
222			for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) {
223			locator->placeMol(latticePos[l], latticeOrt[l], mol);
224			l++;
225			}
226	chuckv	2352
227
228
229	chuckv	2657
230
231	chuckv	2352
232			//fill Hmat
233	chuckv	2657	hmat(0, 0)= latticeConstant;
234	chuckv	2352	hmat(0, 1) = 0.0;
235			hmat(0, 2) = 0.0;
236
237			hmat(1, 0) = 0.0;
238	chuckv	2657	hmat(1, 1) = latticeConstant;
239	chuckv	2352	hmat(1, 2) = 0.0;
240
241			hmat(2, 0) = 0.0;
242			hmat(2, 1) = 0.0;
243	chuckv	2657	hmat(2, 2) = latticeConstant;
244	chuckv	2352
245			//set Hmat
246			NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
247
248
249			//create dumpwriter and write out the coordinates
250			NewInfo->setFinalConfigFileName(outInitFileName);
251			writer = new DumpWriter(NewInfo);
252
253			if (writer == NULL) {
254			std::cerr << "error in creating DumpWriter" << std::endl;
255			exit(1);
256			}
257
258			writer->writeDump();
259			std::cout << "new initial configuration file: " << outInitFileName
260			<< " is generated." << std::endl;
261
262			//delete objects
263
264			//delete oldInfo and oldSimSetup
265
266			if (NewInfo != NULL)
267			delete NewInfo;
268
269			if (writer != NULL)
270	chuckv	2657	delete writer;
271	chuckv	2352	cmdline_parser_free(&args_info);
272			return 0;
273			}
274
275			void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName,
276	chuckv	2657	int components,int* numMol) {
277	chuckv	2352	ifstream oldMdFile;
278			ofstream newMdFile;
279			const int MAXLEN = 65535;
280			char buffer[MAXLEN];
281
282			//create new .md file based on old .md file
283			oldMdFile.open(oldMdFileName.c_str());
284			newMdFile.open(newMdFileName.c_str());
285
286			oldMdFile.getline(buffer, MAXLEN);
287	chuckv	2657
288			int i = 0;
289	chuckv	2352	while (!oldMdFile.eof()) {
290
291			//correct molecule number
292			if (strstr(buffer, "nMol") != NULL) {
293	chuckv	2657	if(i<components){
294			sprintf(buffer, "\tnMol = %i;", numMol[i]);
295	chuckv	2352	newMdFile << buffer << std::endl;
296	chuckv	2657	i++;
297			}
298	chuckv	2352	} else
299			newMdFile << buffer << std::endl;
300
301			oldMdFile.getline(buffer, MAXLEN);
302			}
303
304			oldMdFile.close();
305			newMdFile.close();
306			}
307